A PCR method employing single arbitrarily chosen primers (Arbitrarily primed PCR) generates consistent 'fingerprints' for the mouse genome. These fingerprints include DNA fragment polymorphisms which can be genetically mapped in recombinant inbred lines of mice. This method is very fast and simple and uses only a few nanograms of template DNA. Primers can be used individually or in almost every pairwise combination. There are an average of over four mappable polymorphisms unique to each primer or pair of primers in the BXD recombinant inbred lines. We will be able to use as few as 35 PCR primers to place an additional 2400 DNA polymorphisms on the mouse genetic map in three years using the 26 BXD, 25 AXB and 25 BXA recombinant inbred lines. The accuracy of this map should be better than 5 centiMorgans and should have an average of almost one polymorphism per million base pairs. The genetically assigned AP-PCR fragments will be a valuable resource along with the many restriction fragment length polymorphisms (RFLPs) and PCR based (CA)n polymorphisms already on the map. Those polymorphisms that co-segregate with genetically mapped mutations should be useful for cloning the regions around the genes responsible for such mutations. For instance, the BXD, AXB and BXA recombinant inbred lines are models for susceptibility to certain diseases such as atherosclerosis, glucocorticoid induced cleft palate, some infections and some neoplasms. Mapped AP-PCR polymorphisms will also facilitate the genetic localization of mouse genomic clones that are being assembled into a contig map. Furthermore, due to synteny, information about the mouse genome can sometimes be extended to humans and vice versa.